Hi,

I want to know which Bioconductor package could help me in plotting a heatmap like this:

Heatmap Plotting in R

0

Entering edit mode

Hi,

I want to know which Bioconductor package could help me in plotting a heatmap like this:

4

Entering edit mode

I will try to make a similar figure as yours by ComplexHeatmap package and the explanations are in the comment in the code.

# first generate a matrix with 10 rows and 20 columns mat = matrix(rnorm(200), 10, 20) rownames(mat) = paste0("R", 1:10) colnames(mat) = paste0("C", 1:20) # calculate the correlation matrix cor_mat = cor(t(mat)) # make k-means clustering on rows km = kmeans(mat, 4) # calculate the order of rows after k-means clustering # and also clustering the mean values of the k-groups # Following three lines is not so friendly because it uses # low-level functions, I will try to improve it in the future ht = Heatmap(mat, split = km$cluster) ht = make_row_cluster(ht) row_order = unlist(ht@row_order_list) # color for four subgroups colors = c("red", "blue", "green", "yellow") # now construct a list of heatmaps ht_list = Heatmap(km$cluster, name = "cluster", col = structure(colors, names = 1:4), row_names_side = "left", row_names_gp = gpar(col = colors[km$cluster]), show_heatmap_legend = FALSE, show_column_names = FALSE) + Heatmap(mat, name = "main", col = c("yellow", "#CCCCCC", "blue"), cluster_rows = FALSE, row_order = row_order, show_column_hclust = FALSE, show_row_names = FALSE, show_column_names = FALSE) + Heatmap(runif(10), name = "E1", col = c("white", "black"), show_heatmap_legend = FALSE) + Heatmap(runif(10), name = "E2", col = c("white", "black")) + Heatmap(cor_mat, cluster_columns = FALSE, column_order = row_order, rect_gp = gpar(type = "none"), show_row_names = FALSE, column_names_gp = gpar(col = colors[km$cluster][row_order]), cell_fun = function(j, i, x, y, w, h, col) { if(which(row_order == j) <= which(row_order == i)) grid.rect(x, y, w, h, gp = gpar(fill = col, col = col)) }, heatmap_legend_title = "correlation") draw(ht_list, main_heatmap = "main")

In the heatmap of the correlation matrix, we define `column_order`

to be same as row orders, also we use `cell_fun`

to only plot values corresponding to lower triangles.

Currently, the ComplexHeatmap can not split the rows by adding small gaps (actually it can, but there are some bugs to assign colors to each groups)

Finally, I am still working on the package to let making such complex heatmaps easier.

2

Entering edit mode

If I had to pick a package to try to force into making that heatmap with, it would be the ComplexHeatmap package.

Take some time to skim through its vignette to convince yourself of the same, then spend the next few hours trying to bend it to your will ;-)

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Awesome! Thanks for taking the time to give it a shot ... love the package, by the way!